If I get your question right, the following code should do what you want. I'm sure others will suggest more concise solutions though ;-)

#!perl

use strict;
use warnings;

my @data;

my @buffer;
while (<DATA>) {
    chomp($_);
    s/^\s*(.+?)\s*$/$1/;
    if (/^\s*$/ && scalar(@buffer) > 0) {
        push(@data, [@buffer]);
        @buffer = ();
    } else {
        push(@buffer, split(/\s+/, $_));
    }
}
if (scalar(@buffer) > 0) {
    push(@data, [@buffer]);
    @buffer = ();
}

foreach my $array (@data) {
    print join(", ", @$array), "\n";
}

__DATA__
1    2    3    1    
1    6    4    8    

5    6    9    0    
8    89    5    0    
0    8




7    8    4    6
6    3    79    0

588    7    9    4    
3    9    2    9



9    23    8    0
2    8    98    0

9    7    8    0    
0
[download]

Hope this helps, -gjb-